[gmx-users] Gel Phase in DMPC using Berger force field ??

Thu Dec 13 19:47:12 CET 2007

Dear Eric,

I'm using Berger force field for DOPG (anionic head group).
Is is true for DOPG also?

The following is my MD input.
I'm getting smaller area per lipid (~52 A^2) than expected (~62).

What should I change?

**********************************

; nblist cut-off
rlist                    = 1.6
domain-decomposition     = no

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = PME
rcoulomb-switch          = 0
rcoulomb                 = 1.6
; Relative dielectric constant for the medium and the reaction field
epsilon_r                = 1.0
epsilon_rf               = 1.0
; Method for doing Van der Waals
vdw-type                 = Switch
; cut-off lengths
rvdw-switch              = 1.2
rvdw                     = 1.4

******************************************

On 12/11/07, Eric Jakobsson <jake at ncsa.uiuc.edu> wrote:
>
> Several points:
>
> What is called the Berger force field was
> actually developed by See-Wing Chiu in our lab
> and presented in a 1995 paper.  The Berger et al
> paper tested this force field against another
> candidate and found that it was better, and that
> is the paper that has been cited ever since.
>
> See-Wing did tests of the necessary VDW cut-off
> for accuracy against what seemed like the most
> sensitive test, the value of the dipole potential
> at the water-lipid interface, and concluded that
> one should use a cut-off of at least 18 angstroms.
>
> The van der Waals parameters for the hydrocarbon
> tails were reparameterized in a paper we
> published a few years ago, and in that paper we
> verified that the 18 angstrom cutoff was required
> for an accurate liquid hydrocarbon simulation also.
>
> Recently See-Wing has reparameterized the van der
> Waals parameters in the lipid head groups, using
> specific volumes of liquids comprised of small
> molecules that are part of the head group.  The
> resulting force fields, which retain the partial
> charges of the Berger-Chiu field, work very well
> in replicating x-ray structure factors of lipids
> with various chain compositions, but he has not
> yet tried to do gel phase--that would be
> interesting.  The journal ms. is still sitting on
> my desk, I am afraid, but there is a pretty good
> description of the parameterization in a chapter
> in a book that Scott Feller is editing, which we
> can send on request, as well as the lipid
> complete force field in itself.  We believe it is
> state of the art at this time.
>
> Best,
> Eric
> At 10:22 AM 12/11/2007, you wrote:
> >Hi Steffen,
> >
> >thanks a lot for your reply.
> >>-what are your VdW cutoffs? Berger lipids absolutely need the 0.8/1.4 nm
> >>twin range cutoff for working properly. Are you using PME for
> >>electrostatics?
> >>
> >I used a LJ-cutoff at 1.0nm. That's what was
> >used for the original Berger-Paper (*O Berger, O
> >Edholm and F Jähnig, */Biophysical Journal/ 72:
> >2002-2013 (1997). Shouldn't this be all right?
> >
> >And I used PME (which was indeed not used in the original work.
> >
> >>-how did you set up the pressure coupling?
> >>
> >I used weak coupling (tau=1.0ps)
> >
> >>-900 waters are not really much, the head groups will probably interact
> >>with their mirror images due to pbc. Try a lot more (thought about
> >>10000?) for having a "real" bilayer in a solution.
> >>
> >I also tried with more water, the gel phase did not appear either.
> >
> >> >From my experience, the Berger lipids are well defined for a specific
> >>temperature, but if you go up/down the temperature scale, they are not
> >>really following the experimental values/phase behaviour. By the way:
> >>experimental data on lipid order parameters varies considerably
> >>throughout the complete literature, so don't rely onto that too much as
> >>well.
> >>Sorry for giving more questions than answers, but that's the shitty part
>
> >>with lipid bilayers in MD...
> >>Steffen
> >>
> >Thanks again,
> >Jochen
> >
> >
> >
> >--
> >************************************************
> >Jochen Hub
> >Max Planck Institute for Biophysical Chemistry
> >Computational biomolecular dynamics group
> >Am Fassberg 11
> >D-37077 Goettingen, Germany
> >Email: jhub[at]gwdg.de
> >************************************************
> >_______________________________________________
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> ---------------------------------
> Eric Jakobsson, Ph.D.
> Professor, Department of Molecular and
> Integrative Physiology, and of Biochemistry, and
> of the Center for Biophysics and Computational Biology
> Senior Research Scientist, National Center for Supercomputing Applications
>
> Professor, Beckman Institute for Advanced Science and Technology
> 3261 Beckman Institute, mc251
> University of Illinois, Urbana, IL 61801
> ph. 217-244-2896  Fax 217 244 9757
>
>
>
>
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-- 
Best wishes,

MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
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Office: (850) 645-1334
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